Literature summary for 2.1.1.228 extracted from

Goto-Ito, S.; Ito, T.; Yokoyama, S.
Trm5 and TrmD two enzymes from distinct origins catalyze the identical tRNA modification, m1G37 (2017), Biomolecules, 7, 32 .

Search for more literature for 2.1.1.228

Crystallization (Commentary)

Crystallization (Comment)	Organism
TrmD-tRNA-sinefungin complex, crystal structure determination and analysis. In this complex structure, one TrmD homodimer is complexed with one tRNA molecule, and each TrmD monomer binds a sinefungin molecule. This binding mode is consistent with the previously reported biochemical analysis. When the substrate tRNA interacts with the catalytic pocket of subunit A, the NTDs of subunits A and B, and the neighboring CTD of subunit B, contact the tRNA. The interdomain linker of subunit B forms a helix upon tRNA binding, and participates in the interaction with the substrate tRNA	Haemophilus influenzae

Crystallization (Comment)

Organism

TrmD-tRNA-sinefungin complex, crystal structure determination and analysis. In this complex structure, one TrmD homodimer is complexed with one tRNA molecule, and each TrmD monomer binds a sinefungin molecule. This binding mode is consistent with the previously reported biochemical analysis. When the substrate tRNA interacts with the catalytic pocket of subunit A, the NTDs of subunits A and B, and the neighboring CTD of subunit B, contact the tRNA. The interdomain linker of subunit B forms a helix upon tRNA binding, and participates in the interaction with the substrate tRNA

Haemophilus influenzae

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
additional information	-	additional information	Michaelis-Menten kinetic analysis	Methanocaldococcus jannaschii
additional information	-	additional information	Michaelis-Menten kinetic analysis	Haemophilus influenzae
additional information	-	additional information	Michaelis-Menten kinetic analysis	Escherichia coli
additional information	-	additional information	Michaelis-Menten kinetic analysis	Pyrococcus abyssi

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
S-adenosyl-L-methionine + guanine37 in tRNA	Methanocaldococcus jannaschii	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Haemophilus influenzae	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Escherichia coli	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Pyrococcus abyssi	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Pyrococcus abyssi Orsay	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Methanocaldococcus jannaschii NBRC 100440	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Haemophilus influenzae RD	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Methanocaldococcus jannaschii DSM 2661	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Methanocaldococcus jannaschii ATCC 43067	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Methanocaldococcus jannaschii JAL-1	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Haemophilus influenzae DSM 11121	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Haemophilus influenzae KW20	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Haemophilus influenzae ATCC 51907	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Methanocaldococcus jannaschii JCM 10045	-	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + wyosine37 in tRNAPhe	Pyrococcus abyssi	-	S-adenosyl-L-homocysteine + N1-methylwyosine37 in tRNAPhe	-	?
S-adenosyl-L-methionine + wyosine37 in tRNAPhe	Pyrococcus abyssi Orsay	-	S-adenosyl-L-homocysteine + N1-methylwyosine37 in tRNAPhe	-	?

Organism

Organism	UniProt	Comment	Textmining
Escherichia coli	P0A873	-	-
Haemophilus influenzae	P43912	-	-
Haemophilus influenzae ATCC 51907	P43912	-	-
Haemophilus influenzae DSM 11121	P43912	-	-
Haemophilus influenzae KW20	P43912	-	-
Haemophilus influenzae RD	P43912	-	-
Methanocaldococcus jannaschii	Q58293	i.e. Methanococcus jannaschii	-
Methanocaldococcus jannaschii ATCC 43067	Q58293	i.e. Methanococcus jannaschii	-
Methanocaldococcus jannaschii DSM 2661	Q58293	i.e. Methanococcus jannaschii	-
Methanocaldococcus jannaschii JAL-1	Q58293	i.e. Methanococcus jannaschii	-
Methanocaldococcus jannaschii JCM 10045	Q58293	i.e. Methanococcus jannaschii	-
Methanocaldococcus jannaschii NBRC 100440	Q58293	i.e. Methanococcus jannaschii	-
Pyrococcus abyssi	Q9V2G1	-	-
Pyrococcus abyssi Orsay	Q9V2G1	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
additional information	proposed model for the TrmD enzymatic cycle which consists of the AdoMet-binding, tRNA-binding, and methyl transfer stages, overview. Anticodon-branch recognition and detection of position 37, interaction analysis of TrmD with G36 and G37	Haemophilus influenzae	?	-	-
additional information	proposed model for the TrmD enzymatic cycle which consists of the AdoMet-binding, tRNA-binding, and methyl transfer stages, overview. Anticodon-branch recognition and detection of position 37, interaction analysis of TrmD with G36 and G37	Escherichia coli	?	-	-
additional information	tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA	Methanocaldococcus jannaschii	?	-	-
additional information	tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA	Pyrococcus abyssi	?	-	-
additional information	tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA	Pyrococcus abyssi Orsay	?	-	-
additional information	tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA	Methanocaldococcus jannaschii NBRC 100440	?	-	-
additional information	proposed model for the TrmD enzymatic cycle which consists of the AdoMet-binding, tRNA-binding, and methyl transfer stages, overview. Anticodon-branch recognition and detection of position 37, interaction analysis of TrmD with G36 and G37	Haemophilus influenzae RD	?	-	-
additional information	tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA	Methanocaldococcus jannaschii DSM 2661	?	-	-
additional information	tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA	Methanocaldococcus jannaschii ATCC 43067	?	-	-
additional information	tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA	Methanocaldococcus jannaschii JAL-1	?	-	-
additional information	proposed model for the TrmD enzymatic cycle which consists of the AdoMet-binding, tRNA-binding, and methyl transfer stages, overview. Anticodon-branch recognition and detection of position 37, interaction analysis of TrmD with G36 and G37	Haemophilus influenzae DSM 11121	?	-	-
additional information	proposed model for the TrmD enzymatic cycle which consists of the AdoMet-binding, tRNA-binding, and methyl transfer stages, overview. Anticodon-branch recognition and detection of position 37, interaction analysis of TrmD with G36 and G37	Haemophilus influenzae KW20	?	-	-
additional information	proposed model for the TrmD enzymatic cycle which consists of the AdoMet-binding, tRNA-binding, and methyl transfer stages, overview. Anticodon-branch recognition and detection of position 37, interaction analysis of TrmD with G36 and G37	Haemophilus influenzae ATCC 51907	?	-	-
additional information	tRNA recognition by Trm5, detailed overview. The structure of positions 33-37 in the anticodon loop is largely altered from the canonical tRNA structure, and the target G37 is flipped out into the catalytic pocket formed by the D2 and D3 domains. The flipped G37 is recognized in a guanosine-specific manner by the side chains of Arg145 and Asn265, and the N1-atom (the methylation atom) of G37 is located next to the methyl moiety of AdoMet. The adequate interaction between D1 and tRNA enables the catalytic D2-D3 to perform the m1G37 methylation. The m1G37 methylation is achieved by a sensor-effector mechanism in which the affinity of Trm5 for tRNA increases only when the sensor (D1) confirms the completion of the L-shape formation and the catalytically competent effector (D2-D3) is recruited to the tRNA	Methanocaldococcus jannaschii JCM 10045	?	-	-
S-adenosyl-L-methionine + guanine37 in tRNA	-	Methanocaldococcus jannaschii	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Haemophilus influenzae	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Escherichia coli	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Pyrococcus abyssi	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Pyrococcus abyssi Orsay	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Methanocaldococcus jannaschii NBRC 100440	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Haemophilus influenzae RD	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Methanocaldococcus jannaschii DSM 2661	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Methanocaldococcus jannaschii ATCC 43067	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Methanocaldococcus jannaschii JAL-1	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Haemophilus influenzae DSM 11121	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Haemophilus influenzae KW20	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Haemophilus influenzae ATCC 51907	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Methanocaldococcus jannaschii JCM 10045	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + wyosine37 in tRNAPhe	-	Pyrococcus abyssi	S-adenosyl-L-homocysteine + N1-methylwyosine37 in tRNAPhe	-	?
S-adenosyl-L-methionine + wyosine37 in tRNAPhe	-	Pyrococcus abyssi Orsay	S-adenosyl-L-homocysteine + N1-methylwyosine37 in tRNAPhe	-	?

Subunits

Subunits	Comment	Organism
dimer	deep-trefoil knot structure	Haemophilus influenzae
dimer	deep-trefoil knot structure	Escherichia coli
monomer	Rossmann fold structure	Methanocaldococcus jannaschii
monomer	Rossmann fold structure	Pyrococcus abyssi

Synonyms

Synonyms	Comment	Organism
TAW22	-	Pyrococcus abyssi
TRM5	-	Methanocaldococcus jannaschii
Trm5a	-	Pyrococcus abyssi
trm5b	-	Methanocaldococcus jannaschii
TrmD	-	Haemophilus influenzae
TrmD	-	Escherichia coli
tRNA methyltransferase 5	-	Methanocaldococcus jannaschii
tRNA methyltransferase 5	-	Pyrococcus abyssi
tRNA methyltransferase D	-	Haemophilus influenzae
tRNA methyltransferase D	-	Escherichia coli

Cofactor

Cofactor	Comment	Organism
S-adenosyl-L-methionine	-	Methanocaldococcus jannaschii
S-adenosyl-L-methionine	-	Haemophilus influenzae
S-adenosyl-L-methionine	-	Escherichia coli
S-adenosyl-L-methionine	-	Pyrococcus abyssi

General Information

General Information	Comment	Organism
evolution	the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Enzyme TrmD belongs to the class IV methyltransferases	Haemophilus influenzae
evolution	the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Enzyme TrmD belongs to the class IV methyltransferases.	Escherichia coli
evolution	the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Phylogenetic analyses reveals that the archaeal Trm5s can be classified into three categories: Trm5a, Trm5b, and Trm5c. Trm5a, Trm5b, and Trm5c all perform the N1-methylation of tRNA G37. Enzyme Trm5 belongs to the class I methyltransferases. The Methanocaldococcus jannaschii Trm5b residues involved in the G19:C56 recognition are not conserved in Pyroccocus abyssi Trm5a	Methanocaldococcus jannaschii
evolution	the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Phylogenetic analyses reveals that the archaeal Trm5s can be classified into three categories: Trm5a, Trm5b, and Trm5c. Trm5a, Trm5b, and Trm5c all perform the N1-methylation of tRNA G37. In addition to the methylation of the N1-atom of guanosine, Trm5a catalyzes the methylation of the C7-atom of 4-demethylwyosine, which is the intermediate of the wyosine derivatives found at position 37 of archaeal tRNAPhe. Enzyme Trm5 belongs to the class I methyltransferases. The Methanocaldococcus jannaschii Trm5b residues involved in the G19:C56 recognition are not conserved in Pyroccocus abyssi Trm5a	Pyrococcus abyssi
malfunction	the tRNA mutations, that disrupt the G19:C56 base pair, reduce the activity of full-length Trm5 at 70°C by enhancing the KM values but maintaining the kcat values. The Trm5 mutant with alanine substitutions of the D1 residues, that interact with the tRNA outer corner, has a higher KM value than the wild-type Trm5	Methanocaldococcus jannaschii
malfunction	the tRNA mutations, that disrupt the G19:C56 base pair, reduce the activity of full-length Trm5 at 70°C by enhancing the KM values but maintaining the kcat values. The Trm5 mutant with alanine substitutions of the D1 residues, that interact with the tRNA outer corner, has a higher KM value than the wild-type Trm5	Pyrococcus abyssi
additional information	Trm5 consists of three structural domains: domain 1 (D1), domain 2 (D2), and domain 3 (D3). D1 corresponds to the less-conserved region among Trm5 enzymes from all species, while D2 corresponds to the conserved region. The structure of D2 shares homology with that of TYW2, the tRNA-wybutosine (yW) synthesizing enzyme-2. D3 corresponds to the Rossmann-fold domain containing the AdoMet binding site, and is conserved among the class-I MTases. The D2-D3 fragment alone possesses methyl-transfer activity comparable to that of the full-length enzyme, although the presence of D1 lowers and enhances the KM and kcat values (the Michaelis and catalytic rate constants, respectively, in the Michaelis-Menten equation) for tRNA, respectively, as compared to the D2-D3 fragment. Function of D1, overview. The interaction between the outer-corner of the tRNA and Trm5 D1 is essential to confer sufficiently robust affinity for the tRNA at physiological temperatures	Methanocaldococcus jannaschii
additional information	Trm5 consists of three structural domains: domain 1 (D1), domain 2 (D2), and domain 3 (D3). D1 corresponds to the less-conserved region among Trm5 enzymes from all species, while D2 corresponds to the conserved region. The structures of Pyrococcus abyssi D1 and D2-D3 are similar to those of Methanocaldococcus jannaschii Trm5. The D1 of Pyrococcus abyssi Trm5a behaves independently from D2-D3, as suggested by the fluorescence resonance energy transfer (FRET) analysis. Function of D1, overview. The interaction between the outer-corner of the tRNA and Trm5 D1 is essential to confer sufficiently robust affinity for the tRNA at physiological temperatures	Pyrococcus abyssi
additional information	TrmD consists of the N-terminal domain (NTD, the SPOUT domain) and the TrmD-specific C-terminal domain (CTD). These domains are connected by the interdomain linker. TrmD forms a homodimer, and the interdomain linkers are disordered in both monomers. The trefoil knot at the C-terminal region in the SPOUT domain provides the AdoMet-binding site. Structural changes of TrmD upon AdoMet accommodation. Structure-function analysis, overview	Haemophilus influenzae
additional information	TrmD consists of the N-terminal domain (NTD, the SPOUT domain) and the TrmD-specific C-terminal domain (CTD). These domains are connected by the interdomain linker. TrmD forms a homodimer, and the interdomain linkers are disordered in both monomers. The trefoil knot at the C-terminal region in the SPOUT domain provides the AdoMet-binding site. Structural changes of TrmD upon AdoMet accommodation. Structure-function analysis, overview	Escherichia coli
physiological function	he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome	Methanocaldococcus jannaschii
physiological function	he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome	Haemophilus influenzae
physiological function	he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome	Escherichia coli
physiological function	he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Enzyme Trm5a performs the N1-methylation of tRNA G37, but in addition it also catalyzes the methylation of the C7-atom of 4-demethylwyosine, which is the intermediate of the wyosine derivatives found at position 37 of archaeal tRNAPhe	Pyrococcus abyssi